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Bioconductor - nnSVG (development version)

nnSVG

This is the development version of nnSVG; for the stable release version, see nnSVG.

Scalable identification of spatially variable genes in spatially-resolved transcriptomics data

Bioconductor version: Development (3.22)

Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. The method is based on nearest-neighbor Gaussian processes and uses the BRISC algorithm for model fitting and parameter estimation. Allows identification and ranking of SVGs with flexible length scales across a tissue slide or within spatial domains defined by covariates. Scales linearly with the number of spatial locations and can be applied to datasets containing thousands or more spatial locations.

Author: Lukas M. Weber [aut, cre] ORCID: 0000-0002-3282-1730 , Stephanie C. Hicks [aut] ORCID: 0000-0002-7858-0231

Maintainer: Lukas M. Weber <lmweb012 at gmail.com>

Citation (from within R, enter citation("nnSVG")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("nnSVG")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("nnSVG")
Details biocViews GeneExpression, Preprocessing, SingleCell, Software, Spatial, Transcriptomics Version 1.13.1 In Bioconductor since BioC 3.15 (R-4.2) (3 years) License MIT + file LICENSE Depends R (>= 4.2) Imports SpatialExperiment, SingleCellExperiment, SummarizedExperiment, BRISC, BiocParallel, Matrix, matrixStats, stats, methods System Requirements URL https://github.com/lmweber/nnSVG Bug Reports https://github.com/lmweber/nnSVG/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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